A methods or design paper describes the trial design of a clinical study, i.e., the research methods and data sources, of a planned trial in detail.
It is typically published shortly before the trial actually begins to inform the scientific community that a (usually large and significant) trial is going to be conducted in a particular therapeutic area. This scientific paper is basically the very essence of the study protocol. A research paper, on the other hand, discusses the methods and results obtained in a completed trial.